Library Manager

The Library Manager is a graphical user interface for administrating monomers in the libraries accessed by the Biomolecule Toolkit and BioEddie.

The Biomolecule Toolkit operates with a monomer library that is persisted in its own database schema. This library is typically shared across multiple users and labeled as „Remote”.
BioEddie can operate with the remote library as well as with a „Local” library that resides in the browser cache. The local library is unique to a given browser sessions and cannot be shared with others.

When configured accordingly for BioEddie, switching between local and remote library is possible by clicking on the library selection drop-down images/download/thumbnails/17273024/library_selection_dropdown.png

Selecting a monomer of the library will display a secondary panel showing the full data of a monomer. Modifications to a monomer can be applied here, while actions to add, delete, or duplicate are available from the main monomer table.

Filter monomers

  • Monomers can be filtered based on partial and full matches in the following fields

  • SMILES string

  • Name

  • Abbrevation

  • Natural Analogue

  • Functional Type

  • Matches in their additional data (attribute, value)

Add a new monomer

  • Click on images/download/thumbnails/17273024/add_new.png

  • Select a monomer type in the dropdown

images/download/attachments/17273024/monomer_type_selection.png

  • If PEPTIDE, CHEM or RNA monomer type is selected, then chemical structure can be defined for the monomer. Click on images/download/thumbnails/17273024/pencil.png to open Marvin JS and create the monomer structure with R-groups

  • Define the Name, Abbreviation and the Natural Analogue for the new monomer

images/download/attachments/17273024/monomer_definition.png

  • Select the leaving groups for the corresponding R-groups in the drop-downs

images/download/attachments/17273024/leaving_groups.png

  • Provide additional data if required by clicking on ’Add new’. If the remote library is selected, click on the empty additional data field and select from the registered monomer additional data. Additional data attributes and corresponding values can be removed by clicking on images/download/thumbnails/17273024/delete_additional_data.png

  • Click on Save

The Biomolecule Toolkit uses a controlled list of attributes, hence registering monomers with custom additional data attributes will require you to add these to the controlled list prior to registering monomers using these.
The local library does not exhibit that restriction. Here any additional data attribute can be added for the monomers without restriction.

Clone monomer

  • Hover over a monomer to be deleted

images/download/attachments/17273024/hover_over_monomer.png

  • Click on images/download/thumbnails/17273024/monomer_options.png and delete the monomer

Export monomers

The separate monomer libraries (local and remote) can be exported and downloaded in JSON by clicking on ’Export’ on the Library Manager interface.

Import monomers

Monomer in JSON format can be imported to the local library by clicking on ’Import’ on the interface and selecting the corresponding JSON file.

images/download/attachments/17273024/import-export.png